IMGM Laboratories GmbH - bio

Transcription

IMGM Laboratories GmbH
D JJennifer
Dr.
if K.
K Kuhn
K h
Sales Manager
© IMGM Laboratories 2013
About IMGM Laboratories
•
IMGM Laboratories was founded in 2001
•
IMGM operates as professional provider of advanced
genomic services from research projects to clinical studies
•
Our customers
O
t
come from
f
pharma,
h
CRO bi
CROs,
biotech,
t h
diagnostics, and academia
•
We have formed a strategic partnership with the “Center for
Human Genetics and Laboratory Medicine, Dr. Klein, Dr.
Rost and Colleagues”, one of Germany’s leading diagnostic
laboratories
•
IMGM is accredited according to DIN EN ISO/IEC 17025
including an accreditation for expression analysis based on
whole genome microarrays and quantitative real-time PCR
•
IMGM is Certified Service Provider (CSP) for Agilent and
Affymetrix microarray analysis, and for Life Technologies
Ion Torrent PGM sequencing
Slide 2
IMGM‘s Service Portfolio
Biomarker
Discovery
RNA Services
Biomarker
Discovery
DNA Services
Service
Service
Portfolio
f
Portfolio
Metagenomics
Services
Slide 3
Pharmacogenetics
Services
Biomarker
Discovery
RNA Services
Biomarker
Discovery
DNA Services
S i
Service
Portfolio
Metagenomics
Services
Pharmacogenetics
Services
RNA Services
Slide 4
•
Small RNA / RNA isolation from diverse samples (e.g. FFPE)
•
Small RNA / RNA quality control
(Agilent Bioanalyzer | Nanodrop)
•
Quantitative real-time PCR
(ViiA7, TaqMan assays + arrays, 96- and 384-well blocks)
•
Microarrays
(Agilent and Affymetrix platform)
•
Next Generation Sequencing
(Roche 454 GS FLX+, GS Junior | Illumina MiSeq, GA IIx | Ion Torrent PGM)
mRNA gene expression profiling –
The general workflow at IMGM
Experimental setup
IMGM/Customer
Agilent Bioanalyzer
Catalog/Custom Arrays
Project Consulting
Sample Preparation
Quality Control
Microarrays
Interpretation
of Results
Hit Validation
with qPCR
Report Generation
Bioinformatic
Data Analysis
TaqMan
Technology
Slide 5
Regulated Genes
GeneOntology/Pathways
Characteristics of Agilent
and Affymetrix Microarrays
Array
A
Characteristics
A il t
Agilent
Aff
Affymetrix
ti
Technology
HP inkjet
Photolithography, high density
Flexibility
different formats, e.g. 8x60K
Single arrays
Catalog Arrays
30 species
22 species
Customization
No minimum order quantity at
regular price, eArray Design
Minimum order quantity
(40 – 100 arrays)
Resolution
~1 probe per gene
~26 – 40 probes per gene
Probe Length
60
25
Composition
RefSeq Build 50, Ensemble
Release 52 (Dec 2008),
Unigene Build 216, GenBank
(April 2009), Broad Institute
Human lincRNA catalog and
TUCP transcripts catalog (Nov
2011)
RefSeq Build 51, Ensembl
Release 65 (Dec 2011),
lncRNA db (2011), Broad
Institute Human lincRNA
catalog and TUCP transcripts
catalog (Nov 2011)
> 5 orders of magnitude
< 5 logs orders© IMGM
of magnitude
Laboratories 2013
Linear
Slide
6
dynamic range
Bioinformatic Data Analysis
• Normalization
• Correlation analysis
• Identification of differentially
expressed genes
• Statistical significance
• Biomarker Discovery
• Gene signatures
• Functional analysis of
deregulated genes
• PANTHER ontology
(i l di G
(including
Gene O
Ontology)
t l
)
 Biological processes
 Molecular functions
 Cellular components
 Protein classes
 Pathways
Slide 7
Report Generation
Slide 8
Quantitative real-time PCR –
TaqMan® technology
•
At IMGM, we use TaqMan® assays/arrays
y
y ((Applied Biosystems)
y
) by
y default:
 Highest specificity, greatest sensitivity, and largest dynamic range of any gene
expression technology
 Wide selection of assays for numerous species: >1.2 million predesigned gene
expression assays for 19 species
 Possibility of custom assay/array design and ordering
 Applicable for single samples/biomarkers up to high-throughput studies
Slide 9
Further applications…
•
Determination of biodistribution, e.g.
 Small RNA molecules
 DNA plasmids
 Human cells injected in rodents
 Absolute quantification
 Assay design and validation
 Determination of quality parameters based on OECD guidelines
Slide 10
Biomarker
Discovery
RNA Services
Biomarker
Discovery
DNA Services
S i
Service
Portfolio
Metagenomics
Services
Pharmacogenetics
Services
DNA Services
Slide 11
•
DNA isolation and quality control (e.g. FFPE)
•
CNV analysis
(TaqMan® Copy Number Assays | Agilent aCGH arrays)
•
SNP genotyping
(Pyrosequencing | TaqMan assays | Affymetrix SNP arrays)
•
Sanger sequencing (AB 3730XL 96 capillaries)
•
Next Generation Sequencing
q
g
(Roche 454 FLX(+) + Junior | Illumina MiSeq + GA IIx | Ion Torrent PGM)
•
High-resolution HLA typing
NGS Applications
• De novo sequencing
( i
(viruses,
bacteria,
b t i fungi,
f
i higher
hi h eukaryotes,
k
t
plants, humans etc.)
• Targeted resequencing
((single
g g
genes,, g
gene p
panels or chromosomal regions)
g
)
• Whole exome resequencing
• Whole genome resequencing
• Metagenome
• Gene expression profiling
• Small RNA analysis
• Whole transcriptome analysis
Genome
Transcriptome
Epigenome
• Methylation analysis
• ChIP-Seq (Chromatin immunoprecipitation seq.)
Slide 12
NGS Platforms
Slide 13
Roche
454 GS
Junior
Roche
454 GS
FLX(+)
Titanium
IonTorrent
PGM
Illumina
MiSeq
NGS Platforms
Roche 454 GS Junior
10 hrs/run
~ 1x105 reads/run
400 Q20 bases
35 MB/run
70 MB/day (20hr)
IonTorrent PGM (318)
2 hrs/run
~ 5x106 reads/run
200 Q20 bases
1,000 MB/run
10,000 MB/day (20hr)
Slide 14
Roche
454 GS
Junior
Roche
454 GS
FLX(+)
Titanium
IonTorrent
PGM
Illumina
MiSeq
Roche 454 GS FLX
10 hrs/run
~ 1x106 reads/run
400 Q20 bases
400 MB/run
800 MB/day (20hrs)
Roche 454 GS FLX+
23 hrs/run
~ 1x106 reads/run
600 Q20 bases
600 MB/run
Illumina MiSeq
27 hrs/run
~ 3.3x106 reads/run
2x150 Q30 bases
1,000 MB/run
1,000 MB/day (20hr)
NGS Workflow
Assay
Development
DNA
Preparation
•Primer Design with
IMGM pipeline for
Roche, Illumina
and LifeTech
Illumina
DesignStudio
IonTorrent
AmpliSeq
•Primer Validation
•Qiagen
•Macherey&Nagel
•etc.
Slide 15
Library
Preparation
•Target Enrichment
•Shotgun Library
(mechanical or
enzymatical
fragmentation)
•Amplicon
Amplicon Library
(e.g. single
amplicons,
AccessArray,
TruSeq, AmpliSeq)
•Sample Indexing
Sequence
Generation
Primary Data
Analysis
Secondary
Data Analysis
•Roche GS Junior
•Roche GS FLX
•Roche GS FLX+
•Illumina MiSeq
•Ion Torrent PGM
•Image Processing
•Signal Processing
•Contig generation
•Contig assembly
•Read Mapping
•SNP Calling
•Structural Variation
•Annotation
A
t ti
RNA Services
DNA Services
S i
Service
Portfolio
Metagenomics
Services
Pharmacogenetics
Services
Metagenomics Services
•
Identification of bacterial communities in environmental
and host associated samples such as water, soil,
mucus, feces, etc.
•
In-depth consultation for experimental setup (variable
regions, coverage, sample and library preparation, etc.)
•
Set of universal IMGM primers available
•
Analysis of e.g. up to 6 consecutive variable regions of
the 16S rRNA gene in a single read possible with the
Roche 454 GS FLX+ sequencing platform enabling indepth species detection
© Pearson
P
Education, Inc.
Slide 16
16S rRNA Metagenomics
Example
Short reads – 3 single reads per DNA molecule for 3 variant regions (V1
(V1, V2
V2, V3)
16s variant in V1
16s variant in V2
16s variant in V3
A
A
A
B
B
B
C
Long reads – 1 combined read per DNA molecule for 3 variant regions (V1, V2, V3)
16s variant in V1 – V3
A A A
BAA
B A A
B A B
C B A
Slide 17
IMGM Data
Slide 18
IMGM Data
The distribution of reads for the 780bp amplicon run (> Q30)
Slide 19
IMGM Data
The distribution of reads for the 1
1,050bp
050bp amplicon run (> Q30)
Slide 20
RNA Services
DNA Services
S i
Service
Portfolio
Metagenomics
Services
Pharmacogenetics
Services
Pharmacogenetics Services
Slide 21
•
Using our whole spectrum of small- to high-throughput technologies,
including Pharma – specific applications such as DMET Plus and
U133 Arrays by Affymetrix
•
Further parameters needed for clinical studies available through one
of Europe’s leading Diagnostic Centers within the same building and
under common leadership as IMGM
•
In-depth consultation including gene and polymorphism selection,
clinical protocol, informed consent, appropriate technical approach,
result interpretation,
p
etc.
•
Analytical protocol and report (GCP compliant, e.g. customizable data
formats)
•
Rigorous QA program
Summary
IMGM - YOUR flexible and reliable partner…
Slide 22
•
L
Longstanding
t di experience
i
in
i biomarker
bi
k discovery
di
•
Expert in unique metagenomics NGS sequencing
•
Applying our knowledge to pharmacogenetic services
Summary
IMGM - YOUR flexible and reliable partner…
Slide 23
•
“Personal” project manager, direct communication
•
In-depth project consulting
•
Broad range of up-to-date methods and technologies
•
Delivery of detailed and comprehensive reports fitting your needs
•
Professional quality management system (DAkkS)
•
Working according to GxP Guidelines
•
P f
Professional
i
lb
business
i
relationship
l ti
hi ((e.g. NDA
NDAs, FSA
FSAs, TAT
TATs))
IMGM Team
Dr. Hanns-Georg
Klein
CEO
Dr. Ralph Oehlmann
Dr. Jennifer Kuhn
Stefan Kotschote
Dr. Michael Haberl
Director Business
Development & Marketing
Sales Manager
Head of Laboratory
Head of Quality Assurance
???
Anja Weber
???
Dr. Dirk Haase
Marketing Assistant
Sales Assistant
Project Manager IT
Sabine Brauer
Dr. Marion Deuter
Dr. Cornelia Graf
Dr. Ovidiu Rücker
Dr. Alexandra Dangel
Deputy Head of Laboratory
Head of New Technologies
and Product Development
Project Manager
Project Manager
Project Manager
Slide 24
Melanie Sohns
Andrea Matu
Johannes Tank
Simone Hardel
Head Lab Assistant
Laboratory Assistant
Laboratory Assistant
Assistant New Technologies

IMGM Laboratories GmbH - bio

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